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Motter J, Benckendorff CMM, Westarp S, Sunde-Brown P, Neubauer P, Kurreck A, Miller GJ. Purine nucleoside antibiotics: recent synthetic advances harnessing chemistry and biology. Nat Prod Rep 2024; 41:873-884. [PMID: 38197414 PMCID: PMC11188666 DOI: 10.1039/d3np00051f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Indexed: 01/11/2024]
Abstract
Covering: 2019 to 2023Nucleoside analogues represent one of the most important classes of small molecule pharmaceuticals and their therapeutic development is successfully established within oncology and for the treatment of viral infections. However, there are currently no nucleoside analogues in clinical use for the management of bacterial infections. Despite this, a significant number of clinically recognised nucleoside analogues are known to possess some antibiotic activity, thereby establishing a potential source for new therapeutic discovery in this area. Furthermore, given the rise in antibiotic resistance, the discovery of new clinical candidates remains an urgent global priority and natural product-derived nucleoside analogues may also present a rich source of discovery space for new modalities. This Highlight, covering work published from 2019 to 2023, presents a current perspective surrounding the synthesis of natural purine nucleoside antibiotics. By amalgamating recent efforts from synthetic chemistry with advances in biosynthetic understanding and the use of recombinant enzymes, prospects towards different structural classes of purines are detailed.
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Affiliation(s)
- Jonas Motter
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Caecilie M M Benckendorff
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Peter Sunde-Brown
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Gavin J Miller
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
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Maimone NM, Apaza-Castillo GA, Quecine MC, de Lira SP. Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens. Braz J Microbiol 2024; 55:1863-1882. [PMID: 38421597 PMCID: PMC11153476 DOI: 10.1007/s42770-024-01286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024] Open
Abstract
The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.
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Affiliation(s)
- Naydja Moralles Maimone
- College of Agriculture "Luiz de Queiroz", Department of Exact Sciences, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gladys Angélica Apaza-Castillo
- College of Agriculture "Luiz de Queiroz", Department of Genetics, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Maria Carolina Quecine
- College of Agriculture "Luiz de Queiroz", Department of Genetics, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Simone Possedente de Lira
- College of Agriculture "Luiz de Queiroz", Department of Exact Sciences, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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Bio-Fabrication of ZnONPs from Alkalescent Nucleoside Antibiotic to Control Rice Blast: Impact on Pathogen ( Magnaporthe grisea) and Host (Rice). Int J Mol Sci 2023; 24:ijms24032778. [PMID: 36769154 PMCID: PMC9918085 DOI: 10.3390/ijms24032778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
In the traditional method of the bio-fabrication of zinc oxide nanoparticles (ZnONPs), bacterial strains face metal toxicity and antimicrobial action. In the current study, an alkalescent nucleoside antibiotic was mixed with zinc hexanitrate to fabricate the ZnONPs. An integrated approach of DIAION HP-20 macroporous resin and sephadex LH-20 column chromatography was adopted to separate and purify alkalescent nucleoside AN03 from Streptomyces koyanogensis. Alkalescent nucleoside was confirmed by the Doskochilova solvent system. The bio-fabricated ZnONPs were characterized by using Fourier transform infrared (FTIR), X-ray diffraction (XRD), and transmission electron microscopy (TEM) analyses. The XRD spectrum and the TEM images confirmed the crystallinity and the spherical shape of the ZnONPs with an average size of 22 nm. FTIR analysis showed the presence of functional groups, which confirmed the bio-fabrication of ZnONPs from alkalescent nucleoside ANO3. In-vitro studies showed that 75 μg/mL of ZnONPs had a strong inhibitory zone (28.39 mm) against the Magnaporthe grisea and significantly suppressed the spore germination. SEM and TEM observations respectively revealed that ZnONPs caused breakage in hyphae and could damage the cells of M. grisea. Greenhouse experiments revealed that the foliar spray of ZnONPs could control the rice blast disease by 98%. Results also revealed that ZnONPs had positive effects on the growth of the rice plant. The present study suggested that ZnONPs could be fabricated from microbe-derived nucleoside antibiotics without facing the problems of metal toxicity and antimicrobial action, thus overcoming the problem of pathogen resistance. This could be a potent biocontrol agent in rice blast disease management.
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Yan YC, Zhang H, Hu K, Zhou SM, Chen Q, Qu RY, Yang GF. A mini-review on synthesis and antiviral activity of natural product oxetanocin A derivatives. Bioorg Med Chem 2022; 72:116968. [PMID: 36054994 DOI: 10.1016/j.bmc.2022.116968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022]
Abstract
Oxetanocin A (Oxt-A), a novel oxetanosyl N-glycoside nucleoside, was isolated from Bacillus megaterium in 1986. It carries an oxetane ring on the sugar moiety of the nucleoside scaffold, which contributes to differences in its structure from those of common tetrahydrofuranyl-based nucleosides. In view of the unique 3D-spatial framework, the complete synthesis of Oxt-A has been achieved by multiple research groups. The pharmacological properties of this natural product have also been broadly investigated by pharmacists and chemists since its discovery. Notably, the potential antiviral effect of Oxt-A has captured attention of researchers in the field of antiviral agent development. Furthermore, epidemic outbreaks caused by viruses have been stimulating the preparation and modification of various Oxt-A analogs over the past few decades. However, none of the studies have overviewed the antiviral efficacies of this naturally occurring scaffold yet. Thus, the present review summarizes the synthesis, structural modification, and antiviral activities of Oxt-A and its derivatives. We believe that these comprehensive descriptions will provide a novel perspective for the discovery of antivirus drugs with well-improved performance and pave newer paths for combating sudden public health issues triggered by viruses in the future.
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Affiliation(s)
- Yao-Chao Yan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Hu Zhang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Kai Hu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Shao-Meng Zhou
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Qiong Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Ren-Yu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
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5
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Molecular modelling, DFT, molecular dynamics simulations, synthesis and antimicrobial potential studies of heterocyclic nucleoside mimetics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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6
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Zhang J, Xu J, Li H, Zhang Y, Ma Z, Bechthold A, Yu X. Enhancement of toyocamycin production through increasing supply of precursor GTP in Streptomyces diastatochromogenes 1628. J Basic Microbiol 2022; 62:750-759. [PMID: 35076122 DOI: 10.1002/jobm.202100622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/03/2022] [Accepted: 01/08/2022] [Indexed: 11/07/2022]
Abstract
The nucleoside antibiotic toyocamycin (TM), which is produced by Streptomyces diastatochromogenes 1628, exhibits potent activity against a broad range of phytopathogenic fungi. TM was synthesized through a multi-step reaction, using guanosine triphosphate (GTP) as precursor. Based on a comparison of proteomics data from S. diastatochromogenes 1628 and rifamycin-resistant mutant 1628-T15 with high yield of TM, we determined that the differentially expressed protein X0NBV6 called ribose-phosphate pyrophosphokinase (RHP), which is a rate-limiting enzyme involved in the de novo biosynthesis of GTP, exhibits a higher expression level in mutant 1628-T15. In this study, to elucidate the relationships between RHP, GTP, and TM production, the gene rhp sd encoding RHP was cloned and overexpressed in S. diastatochromogenes strain 1628. The recombinant strain S. diastatochromogenes 1628-RHP exhibited better performance at the transcriptional level of the rhp sd gene, as well as RHP enzymatic activity, intracellular GTP concentration, and TM production, compared to S. diastatochromogenes 1628. Finally, the yield of TM produced by S. diastatochromogenes 1628-RHP (340.2 mg/L) was 133.3% higher than that produced by S. diastatochromogenes1628. Moreover, the transcriptional level of toy genes involved in TM biosynthesis was enhanced due to the overexpression of the rhp sd gene.
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Affiliation(s)
- Jinyao Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Jie Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Huijie Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Yongyong Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute for Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
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7
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Zhang M, Kong L, Gong R, Iorio M, Donadio S, Deng Z, Sosio M, Chen W. Biosynthesis of C-nucleoside antibiotics in actinobacteria: recent advances and future developments. Microb Cell Fact 2022; 21:2. [PMID: 34983520 PMCID: PMC8724604 DOI: 10.1186/s12934-021-01722-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022] Open
Abstract
Epidemic diseases and antibiotic resistance are urgent threats to global health, and human is confronted with an unprecedented dilemma to conquer them by expediting development of new natural product related drugs. C-nucleoside antibiotics, a remarkable group of microbial natural products with diverse biological activities, feature a heterocycle base linked with a ribosyl moiety via an unusual C-glycosidic bond, and have played significant roles in healthcare and for plant protection. Elucidating how nature biosynthesizes such a group of antibiotics has provided the basis for engineered biosynthesis as well as targeted genome mining of more C-nucleoside antibiotics towards improved properties. In this review, we mainly summarize the recent advances on the biosynthesis of C-nucleoside antibiotics, and we also tentatively discuss the future developments on rationally accessing C-nucleoside diversities in a more efficient and economical way via synthetic biology strategies.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Liyuan Kong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rong Gong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | | | | | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.,State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
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8
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Efficient biosynthesis of nucleoside cytokinin angustmycin A containing an unusual sugar system. Nat Commun 2021; 12:6633. [PMID: 34789759 PMCID: PMC8599513 DOI: 10.1038/s41467-021-26928-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/26/2021] [Indexed: 12/25/2022] Open
Abstract
Angustmycin A has anti-mycobacterial and cytokinin activities, and contains an intriguing structure in which an unusual sugar with C5′-C6′ dehydration is linked to adenine via an N-glycosidic bond. However, the logic underlying the biosynthesis of this molecule has long remained obscure. Here, we address angustmycin A biosynthesis by the full deciphering of its pathway. We demonstrate that AgmD, C, A, E, and B function as d-allulose 6-phosphate 3-epimerase, d-allulose 6-phosphate pyrophosphokinase, adenine phosphoallulosyltransferase, phosphoribohydrolase, and phosphatase, respectively, and that these collaboratively catalyze the relay reactions to biosynthesize angustmycin C. Additionally, we provide evidence that AgmF is a noncanonical dehydratase for the final step to angustmycin A via a self-sufficient strategy for cofactor recycling. Finally, we have reconstituted the entire six-enzyme pathway in vitro and in E. coli leading to angustmycin A production. These results expand the enzymatic repertoire regarding natural product biosynthesis, and also open the way for rational and rapid discovery of other angustmycin related antibiotics. Angustmycin A is a nucleoside antibiotic having anti-mycobacterial and cytokinin activities. Here, the authors report the whole pathway leading to angustmycin A biosynthesis in Streptomyces and achieve the heterologous production of angustmycin A in E. coli.
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9
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Berlinck RGS, Crnkovic CM, Gubiani JR, Bernardi DI, Ióca LP, Quintana-Bulla JI. The isolation of water-soluble natural products - challenges, strategies and perspectives. Nat Prod Rep 2021; 39:596-669. [PMID: 34647117 DOI: 10.1039/d1np00037c] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Covering period: up to 2019Water-soluble natural products constitute a relevant group of secondary metabolites notably known for presenting potent biological activities. Examples are aminoglycosides, β-lactam antibiotics, saponins of both terrestrial and marine origin, and marine toxins. Although extensively investigated in the past, particularly during the golden age of antibiotics, hydrophilic fractions have been less scrutinized during the last few decades. This review addresses the possible reasons on why water-soluble metabolites are now under investigated and describes approaches and strategies for the isolation of these natural compounds. It presents examples of several classes of hydrosoluble natural products and how they have been isolated. Novel stationary phases and chromatography techniques are also reviewed, providing a perspective towards a renaissance in the investigation of water-soluble natural products.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Camila M Crnkovic
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Laura P Ióca
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Jairo I Quintana-Bulla
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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10
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Chaurasia H, Singh VK, Mishra R, Yadav AK, Ram NK, Singh P, Singh RK. Molecular modelling, synthesis and antimicrobial evaluation of benzimidazole nucleoside mimetics. Bioorg Chem 2021; 115:105227. [PMID: 34399320 DOI: 10.1016/j.bioorg.2021.105227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 01/23/2023]
Abstract
A series of new N-1-(β-d-ribofuranosyl) benzimidazole derivatives has been designed using in silico methods and synthesized as probable antimicrobial agents. Further, the compounds were assessed for their antibacterial and antifungal activity. Antibacterial screening was done by employing broth micro-dilution method and compounds exhibited excellent inhibitory activity (MIC, 50-1.56 µg/mL) against different human pathogenic bacteria, viz. B. cerus, B. subtilis, S. aureus, E. coli and P. aeruginosa and drug resistant strain (DRS) of E. coli. A great synergistic effect was observed during evaluation of ∑FIC, where a combination study was performed using standard references, viz. chloramphenicol and kanamycin. The MIC data obtained from different methods of combination approach revealed 4-128 fold more potency compared to compounds tested alone. The results clearly indicated the possibility of these compounds as active ingredients of drug regimen used against MDR strains. Antifungal screening were also performed employing two different methods, viz. serial dilution method and zone inhibition method, clearly indicated that compounds were also potentially active against several species of pathogenic fungal strains, viz. A. flavus, A. niger, F. oxysporum and C. albicans. The assessment of structure activity relationship (SAR) clearly revealed that presence of less polar and more hydrophobic substituents positively favours the antibacterial activity, conversely, more polar and hydrophilic substituents favours the antifungal activities. Thus, the results positively endorsed the compounds as potent antibacterial and antifungal agents which could be developed as possible drug regimens.
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Affiliation(s)
- Himani Chaurasia
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Vishal K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Richa Mishra
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Aditya K Yadav
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Nand K Ram
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Prashant Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India.
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Gong R, Yu L, Qin Y, Price NPJ, He X, Deng Z, Chen W. Harnessing synthetic biology-based strategies for engineered biosynthesis of nucleoside natural products in actinobacteria. Biotechnol Adv 2020; 46:107673. [PMID: 33276073 DOI: 10.1016/j.biotechadv.2020.107673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/29/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023]
Abstract
Antibiotic resistance poses an increasing threat to global health, and it is urgent to reverse the present trend by accelerating development of new natural product derived drugs. Nucleoside antibiotics, a valuable family of promising natural products with remarkable structural features and diverse biological activities, have played significant roles in healthcare and for plant protection. Understanding the biosynthesis of these intricate molecules has provided a foundation for bioengineering the microbial cell factory towards yield enhancement and structural diversification. In this review, we summarize the recent progresses in employing synthetic biology-based strategies to improve the production of target nucleoside antibiotics. Moreover, we delineate the advances on rationally accessing the chemical diversities of natural nucleoside antibiotics.
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Affiliation(s)
- Rong Gong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Le Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yini Qin
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Neil P J Price
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
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12
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Draelos MM, Thanapipatsiri A, Sucipto H, Yokoyama K. Cryptic phosphorylation in nucleoside natural product biosynthesis. Nat Chem Biol 2020; 17:213-221. [PMID: 33257873 PMCID: PMC7855722 DOI: 10.1038/s41589-020-00656-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/20/2020] [Indexed: 11/11/2022]
Abstract
Kinases are annotated in many nucleoside biosynthetic gene clusters (BGCs) but generally are considered responsible only for self-resistance. Here, we report an unexpected 2’-phosphorylation of nucleoside biosynthetic intermediates in the nikkomycin and polyoxin pathways. This phosphorylation is a unique cryptic modification as it is introduced in the third of seven steps during aminohexuronic acid (AHA) nucleoside biosynthesis, retained throughout the pathway’s duration, and is removed in the last step of the pathway. Bioinformatic analysis of reported nucleoside BGCs suggests the presence of cryptic phosphorylation in other pathways and the importance of functional characterization of kinases in nucleoside biosynthetic pathways in general. This study also functionally characterized all of the enzymes responsible for AHA biosynthesis and revealed that AHA is constructed via a unique oxidative C-C bond cleavage reaction. The results suggest a divergent biosynthetic mechanism for three classes of antifungal nucleoside natural products.
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Affiliation(s)
| | | | - Hilda Sucipto
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Kenichi Yokoyama
- Department of Chemistry, Duke University, Durham, NC, USA. .,Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
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13
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Zhao Z, Zhang G, Zhang Y, Dou M, Li Y. Fe 3O 4 accelerates tetracycline degradation during anaerobic digestion: Synergistic role of adsorption and microbial metabolism. WATER RESEARCH 2020; 185:116225. [PMID: 32736283 DOI: 10.1016/j.watres.2020.116225] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/11/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Antibiotics contaminants, for example, tetracycline (TC) in the environment have attracted extensive attention around the world, and appropriate treatments for such contaminants are urgently required. In this study, five groups of anaerobic reactors supplemented with different amounts of Fe3O4 were operated periodically to investigate their performance on TC removal. The results showed that Fe3O4 effectively promoted TC removal. Compared with the control reactor, the TC removal efficiency was increased by 7.3% when co-digested with glucose, and increased by 40.4% when mono TC was digested in reactors with 5.0 g/L Fe3O4. Further analysis indicated that the probable mechanism of Fe3O4 promoting TC removal was through TC being adsorbed from the liquid onto Fe3O4, making TC more available for microbes to be biodegraded. Microbial community analysis indicated that the bacteria (Klebsiella, Pseudomonas, and Escherichia) related to TC removal were enriched, which meant more pathways for TC removal were available following the addition of Fe3O4. In addition, in the Fe3O4-supplemented reactors, syntrophic metabolism (between Desulfovibrio and Methanobacterium, Azonexus and Methanobacterium) were possibly established, which played an important role in improving TC removal and CH4 production. The electron transport system data further confirmed these results. The functional gene classification for Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the dominant functions enhanced by Fe3O4 supplementation was microbial metabolic activities.
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Affiliation(s)
- Zisheng Zhao
- School of Ecology and Environment, Zhengzhou University, Kexue Road 100, Zhengzhou 450001, China
| | - Guangyi Zhang
- School of Water Conservancy Science and Engineering, Zhengzhou University, Kexue Road 100, Zhengzhou 450001, China
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Envronmental Engineering (Ministry of Education), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ming Dou
- School of Ecology and Environment, Zhengzhou University, Kexue Road 100, Zhengzhou 450001, China
| | - Yang Li
- School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China.
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14
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Tancos MA, Sechler AJ, Davis EW, Chang JH, Schroeder BK, Murray TD, Rogers EE. The Identification and Conservation of Tunicaminyluracil-Related Biosynthetic Gene Clusters in Several Rathayibacter Species Collected From Australia, Africa, Eurasia, and North America. Front Microbiol 2020; 10:2914. [PMID: 31998251 PMCID: PMC6965331 DOI: 10.3389/fmicb.2019.02914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/03/2019] [Indexed: 01/12/2023] Open
Abstract
Tunicaminyluracil antibiotics are a novel class of toxigenic glycolipids that are synthesized by several soil-associated Actinomycetes. The acquisition of a tunicaminyluracil biosynthetic gene cluster (TGC) in Rathayibacter toxicus has led to the emergence of the only described, naturally occurring tunicaminyluracil-associated mammalian disease, annual ryegrass toxicity of livestock. Endemic to Australia, R. toxicus is obligately vectored by Anguinid seed gall nematodes to the developing seedheads of forage grasses, in which the bacteria synthesize tunicaminyluracils that may subsequently be consumed by livestock and result in high rates of mortality and morbidity. The potential impact of R. toxicus on U.S. agriculture has led the U.S. Department of Agriculture - Animal and Plant Health Inspection Service to list R. toxicus as a Plant Pathogen Select Agent. R. toxicus is the only characterized phytopathogenic bacterium to produce tunicaminyluracils, but numerous R. toxicus-like livestock poisonings outside Australia suggest additional bacterial sources of tunicaminyluracils may exist. To investigate the conservation of the TGC in R. toxicus and whether the TGC is present in other Rathayibacter species, we analyzed genome sequences of members of the Rathayibacter genus. Putative TGCs were identified in genome sequences of R. toxicus, R. iranicus, R. agropyri, and an undescribed South African Rathayibacter species. In the latter three species, the putative TGCs have homologs of tunicaminyluracil-related genes essential for toxin production, but the TGCs differ in gene number and order. The TGCs appear at least partially functional because in contrast to atoxigenic species, TGC-containing Rathayibacter species were each able to tolerate exogenous applications of tunicamycin from Streptomyces chartreusis. The North American R. agropyri TGC shows extensive diversity among the sequenced isolates, with presense/absense polymorphisms in multiple genes or even the whole TGC. R. agropyri TGC structure does not appear to correlate with date or location of isolate collection. The conservation and identification of tunicaminyluracil-related gene clusters in three additional Rathayibacter species isolated from South Africa, the Middle East, and the United States, suggests a wider global distribution of potentially neurotoxigenic plant-associated bacteria. This potential for additional endemic and exotic toxigenic Rathayibacter species could have widespread and severe implications for agriculture.
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Affiliation(s)
- Matthew A. Tancos
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
| | - Aaron J. Sechler
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
| | - Edward W. Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Brenda K. Schroeder
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States
| | - Timothy D. Murray
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Elizabeth E. Rogers
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
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15
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Price NPJ, Jackson MA, Vermillion KE, Blackburn JA, Hartman TM. Rhodium-catalyzed reductive modification of pyrimidine nucleosides, nucleotide phosphates, and sugar nucleotides. Carbohydr Res 2019; 488:107893. [PMID: 31884235 DOI: 10.1016/j.carres.2019.107893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/26/2019] [Accepted: 12/13/2019] [Indexed: 01/27/2023]
Abstract
Nucleosides and nucleotides are a group of small molecule effectors and substrates which include sugar nucleotides, purine and pyrimidine-based nucleotide phosphates, and diverse nucleotide antibiotics. We previously reported that hydrogenation of the nucleotide antibiotic tunicamycin leads to products with reduced toxicity on eukaryotic cells. We now report the hydrogenation of diverse sugar nucleosides, nucleotide phosphates, and pyrimidine nucleotides. UDP-sugars and other uridyl and thymidinyl nucleosides are quantitatively reduced to the corresponding 5,6-dihydro-nucleosides. Cytidyl pyrimidines are reduced, but the major products are the corresponding 5,6-dihydrouridyl nucleosides resulting from a deamination of the cytosine ring.
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Affiliation(s)
- Neil P J Price
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA.
| | - Michael A Jackson
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Karl E Vermillion
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Judith A Blackburn
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Trina M Hartman
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA
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16
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Antiviral effect of sinefungin on in vitro growth of feline herpesvirus type 1. J Antibiot (Tokyo) 2019; 72:981-985. [PMID: 31534199 DOI: 10.1038/s41429-019-0234-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 01/22/2023]
Abstract
Feline herpesvirus type 1 (FHV-1) causes a potentially fatal disease in cats. Through the use of virus inhibition and cytotoxicity assays, sinefungin, a nucleoside antibiotic, was assessed for its potential to inhibit the growth of FHV-1. Sinefungin inhibited in vitro growth of FHV-1 most significantly over other animal viruses, such as feline infectious peritonitis virus, equine herpesvirus, pseudorabies virus and feline calicivirus. Our results revealed that sinefungin specifically suppressed the replication of FHV-1 after its adsorption to the host feline kidney cells in a dose-dependent manner without obvious cytotoxicity to the host cells. This antibiotic can potentially offer a highly effective treatment for animals infected with FHV-1, providing alternative medication to currently available antiviral therapies.
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17
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Niu G, Li Z, Huang P, Tan H. Engineering nucleoside antibiotics toward the development of novel antimicrobial agents. J Antibiot (Tokyo) 2019; 72:906-912. [DOI: 10.1038/s41429-019-0230-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/25/2019] [Accepted: 08/14/2019] [Indexed: 11/09/2022]
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18
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Xu J, Song Z, Xu X, Ma Z, Bechthold A, Yu X. ToyA, a positive pathway-specific regulator for toyocamycin biosynthesis in Streptomyces diastatochromogenes 1628. Appl Microbiol Biotechnol 2019; 103:7071-7084. [DOI: 10.1007/s00253-019-09959-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/29/2019] [Accepted: 06/01/2019] [Indexed: 12/11/2022]
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19
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Yakovleva EP, Kolodyaznaya VA, Boikova IV, Belakhov VV. Influence of Aryl-Substituted Xylose Derivatives on Fermentation of Antifungal Antibiotic Imbricin. RUSS J GEN CHEM+ 2019. [DOI: 10.1134/s1070363218130017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Coordinated Biosynthesis of the Purine Nucleoside Antibiotics Aristeromycin and Coformycin in Actinomycetes. Appl Environ Microbiol 2018; 84:AEM.01860-18. [PMID: 30217843 DOI: 10.1128/aem.01860-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 09/04/2018] [Indexed: 02/05/2023] Open
Abstract
Purine nucleoside antibiotic pairs, concomitantly produced by a single strain, are an important group of microbial natural products. Here, we report a target-directed genome mining approach to elucidate the biosynthesis of the purine nucleoside antibiotic pair aristeromycin (ARM) and coformycin (COF) in Micromonospora haikouensis DSM 45626 (a new producer for ARM and COF) and Streptomyces citricolor NBRC 13005 (a new COF producer). We also provide biochemical data that MacI and MacT function as unusual phosphorylases, catalyzing an irreversible reaction for the tailoring assembly of neplanocin A (NEP-A) and ARM. Moreover, we demonstrate that MacQ is shown to be an adenosine-specific deaminase, likely relieving the potential "excess adenosine" for producing cells. Finally, we report that MacR, an annotated IMP dehydrogenase, is actually an NADPH-dependent GMP reductase, which potentially plays a salvage role for the efficient supply of the precursor pool. Hence, these findings illustrate a fine-tuned pathway for the biosynthesis of ARM and also open the way for the rational search for purine antibiotic pairs.IMPORTANCE ARM and COF are well known for their prominent biological activities and unusual chemical structures; however, the logic of their biosynthesis has long been poorly understood. Actually, the new insights into the ARM and COF pathway will not only enrich the biochemical repertoire for interesting enzymatic reactions but may also lay a solid foundation for the combinatorial biosynthesis of this group of antibiotics via a target-directed genome mining strategy.
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21
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An ATP-Dependent Ligase with Substrate Flexibility Involved in Assembly of the Peptidyl Nucleoside Antibiotic Polyoxin. Appl Environ Microbiol 2018; 84:AEM.00501-18. [PMID: 29703734 DOI: 10.1128/aem.00501-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/19/2018] [Indexed: 11/20/2022] Open
Abstract
Polyoxin (POL) is an unusual peptidyl nucleoside antibiotic, in which the peptidyl moiety and nucleoside skeleton are linked by an amide bond. However, their biosynthesis remains poorly understood. Here, we report the deciphering of PolG as an ATP-dependent ligase responsible for the assembly of POL. A polG mutant is capable of accumulating multiple intermediates, including the peptidyl moiety (carbamoylpolyoxamic acid [CPOAA]) and the nucleoside skeletons (POL-C and the previously overlooked thymine POL-C). We further demonstrate that PolG employs an ATP-dependent mechanism for amide bond formation and that the generation of the hybrid nucleoside antibiotic POL-N is also governed by PolG. Finally, we determined that the deduced ATP-binding sites are functionally essential for PolG and that they are highly conserved in a number of related ATP-dependent ligases. These insights have allowed us to propose a catalytic mechanism for the assembly of peptidyl nucleoside antibiotic via an acyl-phosphate intermediate and have opened the way for the combinatorial biosynthesis/pathway engineering of this group of nucleoside antibiotics.IMPORTANCE POL is well known for its remarkable antifungal bioactivities and unusual structural features. Actually, elucidation of the POL assembly logic not only provides the enzymatic basis for further biosynthetic understanding of related peptidyl nucleoside antibiotics but also contributes to the rational generation of more hybrid nucleoside antibiotics via synthetic biology strategy.
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22
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Sosio M, Gaspari E, Iorio M, Pessina S, Medema MH, Bernasconi A, Simone M, Maffioli SI, Ebright RH, Donadio S. Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics. Cell Chem Biol 2018; 25:540-549.e4. [PMID: 29551347 DOI: 10.1016/j.chembiol.2018.02.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/28/2017] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
Abstract
Pseudouridimycin (PUM) is a selective nucleoside-analog inhibitor of bacterial RNA polymerase with activity against Gram-positive and Gram-negative bacteria. PUM, produced by Streptomyces sp. ID38640, consists of a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 5'-aminopseudouridine. We report the characterization of the PUM gene cluster. Bioinformatic analysis and mutational knockouts of pum genes with analysis of accumulated intermediates, define the PUM biosynthetic pathway. The work provides the first biosynthetic pathway of a C-nucleoside antibiotic and reveals three unexpected features: production of free pseudouridine by the dedicated pseudouridine synthase, PumJ; nucleoside activation by specialized oxidoreductases and aminotransferases; and peptide-bond formation by amide ligases. A central role in the PUM biosynthetic pathway is played by the PumJ, which represents a divergent branch within the TruD family of pseudouridine synthases. PumJ-like sequences are associated with diverse gene clusters likely to govern the biosynthesis of different classes of C-nucleoside antibiotics.
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Affiliation(s)
- Margherita Sosio
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; KtedoGen Srl, Viale Ortles 22/4, 20139 Milan, Italy.
| | | | | | | | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | | | | | - Sonia I Maffioli
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; KtedoGen Srl, Viale Ortles 22/4, 20139 Milan, Italy
| | - Richard H Ebright
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Stefano Donadio
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; KtedoGen Srl, Viale Ortles 22/4, 20139 Milan, Italy
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23
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Casini A, Chang FY, Eluere R, King AM, Young EM, Dudley QM, Karim A, Pratt K, Bristol C, Forget A, Ghodasara A, Warden-Rothman R, Gan R, Cristofaro A, Borujeni AE, Ryu MH, Li J, Kwon YC, Wang H, Tatsis E, Rodriguez-Lopez C, O’Connor S, Medema MH, Fischbach MA, Jewett MC, Voigt C, Gordon DB. A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology. J Am Chem Soc 2018; 140:4302-4316. [DOI: 10.1021/jacs.7b13292] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Arturo Casini
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Fang-Yuan Chang
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Andrew M. King
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Eric M. Young
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Quentin M. Dudley
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty Karim
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Anthony Forget
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amar Ghodasara
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Robert Warden-Rothman
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Rui Gan
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander Cristofaro
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amin Espah Borujeni
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Min-Hyung Ryu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Jian Li
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Yong-Chan Kwon
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - He Wang
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Evangelos Tatsis
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - Sarah O’Connor
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Michael A. Fischbach
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Bioengineering and Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, California 94305, United States
| | - Michael C. Jewett
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher Voigt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - D. Benjamin Gordon
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
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24
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Selective catalytic hydrogenation of the N-acyl and uridyl double bonds in the tunicamycin family of protein N-glycosylation inhibitors. J Antibiot (Tokyo) 2017; 70:1122-1128. [DOI: 10.1038/ja.2017.141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 02/04/2023]
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25
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Biosynthesis of 2'-Chloropentostatin and 2'-Amino-2'-Deoxyadenosine Highlights a Single Gene Cluster Responsible for Two Independent Pathways in Actinomadura sp. Strain ATCC 39365. Appl Environ Microbiol 2017; 83:AEM.00078-17. [PMID: 28258148 DOI: 10.1128/aem.00078-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/26/2017] [Indexed: 01/30/2023] Open
Abstract
2'-Chloropentostatin (2'-Cl PTN, 2'-chloro-2'-deoxycoformycin) and 2'-amino-2'-deoxyadenosine (2'-amino dA) are two adenosine-derived nucleoside antibiotics coproduced by Actinomadura sp. strain ATCC 39365. 2'-Cl PTN is a potent adenosine deaminase (ADA) inhibitor featuring an intriguing 1,3-diazepine ring, as well as a chlorination at C-2' of ribose, and 2'-amino dA is an adenosine analog showing bioactivity against RNA-type virus infection. However, the biosynthetic logic of them has remained poorly understood. Here, we report the identification of a single gene cluster (ada) essential for the biosynthesis of 2'-Cl PTN and 2'-amino dA. Further systematic genetic investigations suggest that 2'-Cl PTN and 2'-amino dA are biosynthesized by independent pathways. Moreover, we provide evidence that a predicted cation/H+ antiporter, AdaE, is involved in the chlorination step during 2'-Cl PTN biosynthesis. Notably, we demonstrate that 2'-amino dA biosynthesis is initiated by a Nudix hydrolase, AdaJ, catalyzing the hydrolysis of ATP. Finally, we reveal that the host ADA (designated ADA1), capable of converting adenosine/2'-amino dA to inosine/2'-amino dI, is not very sensitive to the powerful ADA inhibitor pentostatin. These findings provide a basis for the further rational pathway engineering of 2'-Cl PTN and 2'-amino dA production.IMPORTANCE 2'-Cl PTN/PTN and 2'-amino dA have captivated the great interests of scientists, owing to their unusual chemical structures and remarkable bioactivities. However, the precise logic for their biosynthesis has been elusive for decades. Actually, the identification and elucidation of their biosynthetic pathways not only enrich the biochemical repertoire of novel enzymatic reactions but may also lay solid foundations for the pathway engineering and combinatorial biosynthesis of this family of purine nucleoside antibiotics to generate novel hybrid analogs with improved features.
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26
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Nature's combinatorial biosynthesis and recently engineered production of nucleoside antibiotics in Streptomyces. World J Microbiol Biotechnol 2017; 33:66. [PMID: 28260195 DOI: 10.1007/s11274-017-2233-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/22/2017] [Indexed: 10/20/2022]
Abstract
Modified nucleosides produced by Streptomyces and related actinomycetes are widely used in agriculture and medicine as antibacterial, antifungal, anticancer and antiviral agents. These specialized small-molecule metabolites are biosynthesized by complex enzymatic machineries encoded within gene clusters in the genome. The past decade has witnessed a burst of reports defining the key metabolic processes involved in the biosynthesis of several distinct families of nucleoside antibiotics. Furthermore, genome sequencing of various Streptomyces species has dramatically increased over recent years. Potential biosynthetic gene clusters for novel nucleoside antibiotics are now apparent by analysis of these genomes. Here we revisit strategies for production improvement of nucleoside antibiotics that have defined mechanisms of action, and are in clinical or agricultural use. We summarize the progress for genetically manipulating biosynthetic pathways for structural diversification of nucleoside antibiotics. Microorganism-based biosynthetic examples are provided and organized under genetic principles and metabolic engineering guidelines. We show perspectives on the future of combinatorial biosynthesis, and present a working model for discovery of novel nucleoside natural products in Streptomyces.
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27
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An Unusual Protector-Protégé Strategy for the Biosynthesis of Purine Nucleoside Antibiotics. Cell Chem Biol 2017; 24:171-181. [PMID: 28111097 DOI: 10.1016/j.chembiol.2016.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/07/2016] [Accepted: 12/19/2016] [Indexed: 01/17/2023]
Abstract
Pentostatin (PTN, deoxycoformycin) and arabinofuranosyladenine (Ara-A, vidarabine) are purine nucleoside antibiotics used clinically to treat hematological cancers and human DNA virus infections, respectively. PTN has a 1,3-diazepine ring, and Ara-A is an adenosine analog with an intriguing epimerization at the C-2' hydroxyl group. However, the logic underlying the biosynthesis of these interesting molecules has long remained elusive. Here, we report that the biosynthesis of PTN and Ara-A employs an unusual protector-protégé strategy. To our surprise, we determined that a single gene cluster governs PTN and Ara-A biosynthesis via two independent pathways. Moreover, we verified that PenB functions as a reversible oxidoreductase for the final step of PTN. Remarkably, we provided the first direct biochemical evidence that PTN can protect Ara-A from deamination by selective inhibition of the host adenosine deaminase. These findings expand our knowledge of natural product biosynthesis and open the way for target-directed genome mining of Ara-A/PTN-related antibiotics.
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28
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He N, Wu P, Lei Y, Xu B, Zhu X, Xu G, Gao Y, Qi J, Deng Z, Tang G, Chen W, Xiao Y. Construction of an octosyl acid backbone catalyzed by a radical S-adenosylmethionine enzyme and a phosphatase in the biosynthesis of high-carbon sugar nucleoside antibiotics. Chem Sci 2017; 8:444-451. [PMID: 28451191 PMCID: PMC5365060 DOI: 10.1039/c6sc01826b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/17/2016] [Indexed: 01/26/2023] Open
Abstract
Unique bicyclic octosyl uronic acid nucleosides include ezomycin, malayamycin, and octosyl acid (OA). They are structurally characterized by OA, an unusual 8-carbon furanosyl nucleoside core proposed to be the precursor to polyoxin and nikkomycin. Despite the well-known bioactivity of these nucleoside antibiotics, the biosynthesis of OA has not been elucidated yet. Here we report the two pivotal enzymatic steps in the polyoxin biosynthetic pathway leading to the identification of OA as a key intermediate. Our data suggest that this intermediate is formed via a free radical reaction catalyzed by the radical S-adenosylmethionine (SAM) enzyme, PolH, and using 3'-enolpyruvyl uridine 5'-monophosphate (3'-EUMP) as a substrate. Subsequent dephosphorylation catalyzed by phosphatase PolJ converts the resulting octosyl acid 5'-phosphate (OAP) to OA. These results provide, for the first time, significant in vitro evidence for the biosynthetic origins of the C8 backbone of OA.
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Affiliation(s)
- Nisha He
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Pan Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Yongxing Lei
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Baofu Xu
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Xiaochen Zhu
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
| | - Gudan Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Yaojie Gao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Jianzhao Qi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Gongli Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
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Adamek M, Spohn M, Stegmann E, Ziemert N. Mining Bacterial Genomes for Secondary Metabolite Gene Clusters. Methods Mol Biol 2017; 1520:23-47. [PMID: 27873244 DOI: 10.1007/978-1-4939-6634-9_2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
With the emergence of bacterial resistance against frequently used antibiotics, novel antibacterial compounds are urgently needed. Traditional bioactivity-guided drug discovery strategies involve laborious screening efforts and display high rediscovery rates. With the progress in next generation sequencing methods and the knowledge that the majority of antibiotics in clinical use are produced as secondary metabolites by bacteria, mining bacterial genomes for secondary metabolites with antimicrobial activity is a promising approach, which can guide a more time and cost-effective identification of novel compounds. However, what sounds easy to accomplish, comes with several challenges. To date, several tools for the prediction of secondary metabolite gene clusters are available, some of which are based on the detection of signature genes, while others are searching for specific patterns in gene content or regulation.Apart from the mere identification of gene clusters, several other factors such as determining cluster boundaries and assessing the novelty of the detected cluster are important. For this purpose, comparison of the predicted secondary metabolite genes with different cluster and compound databases is necessary. Furthermore, it is advisable to classify detected clusters into gene cluster families. So far, there is no standardized procedure for genome mining; however, different approaches to overcome all of these challenges exist and are addressed in this chapter. We give practical guidance on the workflow for secondary metabolite gene cluster identification, which includes the determination of gene cluster boundaries, addresses problems occurring with the use of draft genomes, and gives an outlook on the different methods for gene cluster classification. Based on comprehensible examples a protocol is set, which should enable the readers to mine their own genome data for interesting secondary metabolites.
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Affiliation(s)
- Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, 72076, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, 72076, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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Serpi M, Ferrari V, Pertusati F. Nucleoside Derived Antibiotics to Fight Microbial Drug Resistance: New Utilities for an Established Class of Drugs? J Med Chem 2016; 59:10343-10382. [PMID: 27607900 DOI: 10.1021/acs.jmedchem.6b00325] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel antibiotics are urgently needed to combat the rise of infections due to drug-resistant microorganisms. Numerous natural nucleosides and their synthetically modified analogues have been reported to have moderate to good antibiotic activity against different bacterial and fungal strains. Nucleoside-based compounds target several crucial processes of bacterial and fungal cells such as nucleoside metabolism and cell wall, nucleic acid, and protein biosynthesis. Nucleoside analogues have also been shown to target many other bacterial and fungal cellular processes although these are not well characterized and may therefore represent opportunities to discover new drugs with unique mechanisms of action. In this Perspective, we demonstrate that nucleoside analogues, cornerstones of anticancer and antiviral treatments, also have great potential to be repurposed as antibiotics so that an old drug can learn new tricks.
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Affiliation(s)
- Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Valentina Ferrari
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
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Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes. Nat Chem Biol 2016; 12:905-907. [PMID: 27642865 PMCID: PMC5069167 DOI: 10.1038/nchembio.2187] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 08/16/2016] [Indexed: 01/04/2023]
Abstract
Nikkomycins and polyoxins are antifungal peptidylnucleoside antibiotics active against human and plant pathogens. Here we report that during peptidylnucleoside biosynthesis in Streptomyces cacaoi and S. tendae, the C5' extension of the nucleoside essential for downstream structural diversification is catalyzed by a conserved radical S-adenosyl-L-methionine (SAM) enzyme, PolH or NikJ. This is distinct from the nucleophilic mechanism reported for antibacterial nucleosides and represents a new mechanism of nucleoside natural product biosynthesis.
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Qi J, Wan D, Ma H, Liu Y, Gong R, Qu X, Sun Y, Deng Z, Chen W. Deciphering Carbamoylpolyoxamic Acid Biosynthesis Reveals Unusual Acetylation Cycle Associated with Tandem Reduction and Sequential Hydroxylation. Cell Chem Biol 2016; 23:935-44. [DOI: 10.1016/j.chembiol.2016.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 01/27/2023]
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An unusual UMP C-5 methylase in nucleoside antibiotic polyoxin biosynthesis. Protein Cell 2016; 7:673-83. [PMID: 27412636 PMCID: PMC5003785 DOI: 10.1007/s13238-016-0289-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/14/2016] [Indexed: 11/04/2022] Open
Abstract
Polyoxin is a group of structurally-related peptidyl nucleoside antibiotics bearing C-5 modifications on the nucleoside skeleton. Although the structural diversity and bioactivity preference of polyoxin are, to some extent, affected by such modifications, the biosynthetic logic for their occurence remains obscure. Here we report the identification of PolB in polyoxin pathway as an unusual UMP C-5 methylase with thymidylate synthase activity which is responsible for the C-5 methylation of the nucleoside skeleton. To probe its molecular mechanism, we determined the crystal structures of PolB alone and in complexes with 5-Br UMP and 5-Br dUMP at 2.15 Å, 1.76 Å and 2.28 Å resolutions, respectively. Loop 1 (residues 117–131), Loop 2 (residues 192–201) and the substrate recognition peptide (residues 94–102) of PolB exhibit considerable conformational flexibility and adopt distinct structures upon binding to different substrate analogs. Consistent with the structural findings, a PolB homolog that harbors an identical function from Streptomyces viridochromogenes DSM 40736 was identified. The discovery of UMP C5-methylase opens the way to rational pathway engineering for polyoxin component optimization, and will also enrich the toolbox for natural nucleotide chemistry.
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